Package: aroma.core Class RawGenomicSignals
data.frame
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RichDataFrame
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RawGenomicSignals
Directly known subclasses: AbstractCNData, AbstractPSCNData, NonPairedPSCNData, PairedPSCNData, RawAlleleBFractions, RawCopyNumbers, RawMirroredAlleleBFractions, RawSequenceReads, SegmentedAlleleBFractions, SegmentedCopyNumbers
public class RawGenomicSignals extends RichDataFrame
RawGenomicSignals(y=NULL, x=NULL, w=NULL, chromosome=0L, name=NULL, ...)
An (optional) integer
specifying the chromosome for
these genomic signals.
An (optional) character
string specifying the sample name.
Not used.
Methods:
* |
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+ |
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addBy |
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append |
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as.data.frame |
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binnedSmoothing |
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divideBy |
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drawDensity |
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estimateStandardDeviation |
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gaussianSmoothing |
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getChromosome |
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getChromosomes |
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getPositions |
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getSigma |
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getSignals |
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getWeights |
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getXScale |
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getYScale |
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hasWeights |
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kernelSmoothing |
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lines |
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multiplyBy |
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nbrOfChromosomes |
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nbrOfLoci |
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plot |
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points |
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segmentByCBS |
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segmentByGLAD |
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segmentByHaarSeg |
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segmentByMPCBS |
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setSigma |
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setSignals |
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setWeights |
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setXScale |
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setYScale |
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signalRange |
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sort |
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subtractBy |
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xMax |
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xMin |
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xRange |
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xSeq |
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yMax |
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yMin |
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yRange |
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Methods inherited from RichDataFrame: $, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame: $, $<-, Math, Ops, Summary, [, [<-, [[, [[<-, aggregate, anyDuplicated, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, attachLocally, by, callSegmentationOutliers, cbind, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, split, split<-, stack, str, subset, summary, t, tail, transform, unique, unstack, unwrap, within, wrap, writeDataFrame